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    ZGPAT zinc finger CCCH-type and G-patch domain containing [ Homo sapiens (human) ]

    Gene ID: 84619, updated on 5-Mar-2024

    Summary

    Official Symbol
    ZGPATprovided by HGNC
    Official Full Name
    zinc finger CCCH-type and G-patch domain containingprovided by HGNC
    Primary source
    HGNC:HGNC:15948
    See related
    Ensembl:ENSG00000197114 MIM:619577; AllianceGenome:HGNC:15948
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ZIP; ZC3H9; GPATC6; GPATCH6; ZC3HDC9; KIAA1847
    Summary
    Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of epidermal growth factor-activated receptor activity and negative regulation of transcription by RNA polymerase II. Located in nucleoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in liver (RPKM 22.1), kidney (RPKM 17.5) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    Location:
    20q13.33
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63707442..63736142)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65527749..65556418)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62338794..62367494)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RTEL1-TNFRSF6B readthrough (NMD candidate) Neighboring gene uncharacterized LOC124904954 Neighboring gene regulator of telomere elongation helicase 1 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62307938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62313341-62314065 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62314792-62315516 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62320674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62330893-62331773 Neighboring gene TNF receptor superfamily member 6b Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13178 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62339316-62340276 Neighboring gene ADP ribosylation factor related protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62347847-62348348 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:62359961-62360460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62363158-62363701 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62363702-62364244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62368201-62369118 Neighboring gene LIME1 eExon liver enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13186 Neighboring gene ZBTB46 antisense RNA 2 Neighboring gene SLC2A4 regulator Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62383144-62384094 Neighboring gene Lck interacting transmembrane adaptor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62384095-62385046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62385047-62385996 Neighboring gene zinc finger and BTB domain containing 46 Neighboring gene uncharacterized LOC124904956 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62401989-62402163

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog
    Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease.
    EBI GWAS Catalog
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of zinc finger, CCCH-type with G patch domain (ZGPAT) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Vpr vpr HIV-1 Vpr induces the degradation of ZIP/sZIP through the DCAF1 ubiquitin ligase, while VprQ65R mutant impairs the Vpr-induced degradation of ZIP/sZIP PubMed
    vpr HIV-1 Vpr forms a complex by recruiting RbAp46, HAT1, ZIP/sZIP, and Cul4A PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: LIME1

    Clone Names

    • KIAA1847, MGC44880

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    zinc finger CCCH-type with G patch domain-containing protein
    Names
    g patch domain-containing protein 6
    zinc finger CCCH domain-containing protein 9
    zinc finger and G patch domain-containing protein
    zinc finger, CCCH-type with G patch domain

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001083113.2NP_001076582.1  zinc finger CCCH-type with G patch domain-containing protein isoform c

      See identical proteins and their annotated locations for NP_001076582.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the middle portion of the coding region, compared to variant 1. This results in a shorter protein (isoform c), compared to isoform a. Variants 3, 4 and 5 encode the same isoform (c).
      Source sequence(s)
      AB058750, BC019338, DA252406
      Consensus CDS
      CCDS13535.1
      UniProtKB/TrEMBL
      A0A0S2Z5X3, A0A0S2Z6H0
      Related
      ENSP00000391176.1, ENST00000448100.6
      Conserved Domains (3) summary
      cd04508
      Location:221251
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      smart00356
      Location:178199
      ZnF_C3H1; zinc finger
      pfam01585
      Location:313354
      G-patch; G-patch domain
    2. NM_001195653.2NP_001182582.1  zinc finger CCCH-type with G patch domain-containing protein isoform c

      See identical proteins and their annotated locations for NP_001182582.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and uses an alternate in-frame splice site in the middle portion of the coding region, compared to variant 1. This results in a shorter protein (isoform c), compared to isoform a. Variants 3, 4 and 5 encode the same isoform (c).
      Source sequence(s)
      AK314726, BC019338, BC032612
      Consensus CDS
      CCDS13535.1
      UniProtKB/TrEMBL
      A0A0S2Z5X3, A0A0S2Z6H0
      Related
      ENSP00000358984.3, ENST00000369967.7
      Conserved Domains (3) summary
      cd04508
      Location:221251
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      smart00356
      Location:178199
      ZnF_C3H1; zinc finger
      pfam01585
      Location:313354
      G-patch; G-patch domain
    3. NM_001195654.2NP_001182583.1  zinc finger CCCH-type with G patch domain-containing protein isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) uses two alternate in-frame splice sites in the middle portion of the coding region, compared to variant 1. This results in a shorter protein (isoform d), compared to isoform a.
      Source sequence(s)
      BC019338, BC032612, DA055150
      Consensus CDS
      CCDS56203.1
      UniProtKB/TrEMBL
      A0A0S2Z6H0
      Related
      ENSP00000349634.4, ENST00000357119.8
      Conserved Domains (3) summary
      cd04508
      Location:221251
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      smart00356
      Location:178199
      ZnF_C3H1; zinc finger
      pfam01585
      Location:304345
      G-patch; G-patch domain
    4. NM_032527.5NP_115916.3  zinc finger CCCH-type with G patch domain-containing protein isoform a

      See identical proteins and their annotated locations for NP_115916.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AK027878, BC019338, BC032612, DA055150
      Consensus CDS
      CCDS13534.1
      UniProtKB/Swiss-Prot
      E1P5K1, Q4VXN9, Q5JWI9, Q5JWJ0, Q8N5A5, Q8NC55, Q8WUV4, Q96JI0, Q96JU4, Q9H401
      UniProtKB/TrEMBL
      A0A0S2Z6H0
      Related
      ENSP00000332013.5, ENST00000328969.5
      Conserved Domains (3) summary
      cd04508
      Location:221251
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      smart00356
      Location:178199
      ZnF_C3H1; zinc finger
      pfam01585
      Location:333374
      G-patch; G-patch domain
    5. NM_181485.3NP_852150.2  zinc finger CCCH-type with G patch domain-containing protein isoform c

      See identical proteins and their annotated locations for NP_852150.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the middle portion of the coding region, compared to variant 1. This results in a shorter protein (isoform c), compared to isoform a. Variants 3, 4 and 5 encode the same isoform (c).
      Source sequence(s)
      AL121845, BC019338, BC032612, DA848516
      Consensus CDS
      CCDS13535.1
      UniProtKB/TrEMBL
      A0A0S2Z5X3, A0A0S2Z6H0
      Related
      ENSP00000348242.6, ENST00000355969.11
      Conserved Domains (3) summary
      cd04508
      Location:221251
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      smart00356
      Location:178199
      ZnF_C3H1; zinc finger
      pfam01585
      Location:313354
      G-patch; G-patch domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      63707442..63736142
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      65527749..65556418
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_181484.1: Suppressed sequence

      Description
      NM_181484.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.